The New York imam at the centre of plans to build an Islamic centre near Ground Zero said today that "disaster" had been narrowly averted over the planned burning of copies of the Qur'an by a Florida pastor.

In his first comments since the row escalated into a national and international crisis, Feisal Abdul Rauf said the act could have provoked fresh terrorist attacks against the US.

After a series of conflicting and confusing statements over the previous 48 hours, Pastor Terry Jones finally confirmed yesterday that he was not going ahead with his plan, "not today, not ever".

But some damage had been done and thousands of protesters took to the streets in Afghanistan today for the third day in a row. Three were shot, one of them seriously, amid threats to storm US military bases.

While media attention focused on Jones, desecration of Qur'ans took place elsewhere across the US on the ninth anniversary of the 9/11 attacks. Copies of the Muslim holy book were torn up in New York and Washington, and burned in Tennessee and Kansas.

Little publicity was given to these events, with the major US networks taking a decision not to cover any such stunts. Most said in advance that they would not have broadcast Jones's event.

With anti-Muslim sentiment reaching levels not witnessed in the US at any point since the 2001 al-Qaida attacks on New York and Washington, rival rallies were held in New York for and against Rauf's proposed cultural centre.

In an interview with ABC, Rauf said Jones's planned burning "would have strengthened the radicals. It would have enhanced the possibility of terrorist acts against America and American interests."

He said he intended to go ahead with the centre, and expressed concern about a rise in anti-Muslim feeling across the US. "How else would you describe the fact that mosques around the country are now being attacked?" Rauf said.

The imam did not meet Jones, who flew to New York from Florida on Friday. Jones, in an apparent face-saving exercise, claimed he had abandoned his burning ceremony because Rauf had agreed to meet him and to move the location of his centre. Rauf denied the claims.

Remembrance ceremonies for 9/11 had until this weekend been marked mainly by shows of unity. But the divisions over the planned Islamic centre have heightened tensions.

Members of the far-right English Defence League flew to New York to join the rally against the centre. The group's leader, who goes by the pseudonym Tommy Robinson, reportedly was refused entry at JFK airport and was put on a plane back to the UK, according to the anti-Islam Gates of Vienna website. But others in the group were allowed in.

Members of the EDL and other European rightwing organisations, including Geert Wilders, the Dutch leader of the Freedom party (PVV), were pictured at the demonstration in lower Manhattan holding banners with the slogans "No Mosque at Ground Zero", "The more Islam, the less freedom", "No Sharia" and "No Surrender".

One of the American organisers of the campaign against the centre, Pamela Geller, has in the past praised the EDL and said she has been in contact with the group.

Barack Obama, at a 9/11 ceremony at the Pentagon yesterday, repeated his calls for restraint, saying: "As Americans, we are not – and never will be – at war with Islam." He said the US would stay true to its tradition as a diverse and tolerant nation. But his pleas went unheeded in isolated ceremonies across the country.

Websites in Tennessee showed pictures of two pastors, Bob Old and Danny Allen, burning copies of the Qur'an in Springfield. The Daily Beast website reported that in Topeka, Kansas, members of the Westboro church burned a Qur'an in front of the media.

A Christian group tore pages from the Qur'an outside the White House. In New York, an unidentified man tore pages from the Qur'an and set them alight outside the planned Islamic centre.